Regardless of flight details in to Jamaica, since you have a reservation at Couples for a specific date they will be aware that you are arriving on that day and your name will be on their list. Time of arrival is sort of irrelevant to them as they have busses leaving all day at more or less regular intervals. Once you have cleared immigration and customs, find you way to the Couples lounge (easy to find, not a very large airport) and they will take care of you from there. No worries, you will be on your way to your resort in short order.

On check in you will fill in your airline, flight number and time out of Jamaica. This will allow them to arrange for transport back to the airport and inform you of when to have your bags ready for pick up to check out on your departure date. Pretty simple and straight forward process in both directions. Again, no worries.

We just called 1-800-COUPLES three days ahead of time and it worked out great. We even had to call them back the morning of out trip when our flight was moved from 9:30 to 1:30. They were waiting for us in the lounge when we arrived. I barely had time to grab a Red Stripe before they whisked us off to the resort.

I don't think it matters if you have your hotel reservations, they know when you arrive at the hotel. The flight times don't correlate with check in times at the hotels. You can show the shuttle driver your itinerary for the hotel you need to be transported to. Or, if you would need to confirm, call the hotel and ask.